Plasmids play important roles in microbial evolution and also in the spread of antibiotic resistance. Plasmid sequences are extensively studied from clinical isolates but rarely from the environment with a metagenomic approach focused on the plasmid fraction referred to as the plasmidome. A clear challenge in this context is to define a workflow for discriminating plasmids from chromosomal contaminants existing in the plasmidome. For this purpose, we benchmarked existing tools from assembly to detection of the plasmids by reference-free methods (cBar and PlasFlow) and database-guided approaches. Our simulations took into account short-reads alone or combined with moderate long-reads like those actually generated in environmental genomics experiments. This benchmark allowed us to select the best tools for limiting false-positives associated to plasmid prediction tools and a combination of reference-guided methods based on plasmid and bacterial databases.

中文翻译：

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通过鸟枪测序从环境 DNA 中重建质粒：哪种生物信息学工作流程？

质粒在微生物进化和抗生素耐药性传播中发挥着重要作用。质粒序列是从临床分离株中广泛研究的，但很少从环境中研究，宏基因组方法侧重于称为质粒组的质粒部分。在这种情况下，一个明显的挑战是定义一个工作流程，用于从质粒组中存在的染色体污染物中区分质粒。为此，我们通过无参考方法（cBar 和 PlasFlow）和数据库引导方法对从组装到质粒检测的现有工具进行了基准测试。我们的模拟单独考虑了短读长或与环境基因组学实验中实际产生的中等长读长相结合。